Unsolved

hi everyone;

Hard time installing rosetta on ubuntu 11.10.
different problems, very frustrating.

Linux 3.0
ubuntu 11.10
python 2.7
gcc 4.6

Here is the recent one；

/tmp/ccIDDP8t.s: Assembler messages:
/tmp/ccIDDP8t.s: Error: .size expression for _ZN7utility7options15VectorOption_T_INS0_19PathVectorOptionKeyENS_4file8PathNameEE5valueERKS4_ does not evaluate to a constant
/tmp/ccIDDP8t.s: Error: .size expression for _ZSt22__uninitialized_move_aIPN7utility7options10PathOptionES3_SaIS2_EET0_T_S6_S5_RT1_ does not evaluate to a constant

I am trying to use loopmodel to fold a linear peptide of 216 standard aa (obtained from the only existing data: fasta file, by using either the BuildPeptide or FragmentPicker executables of rosetta3.3).

I first tried "loopmodel.mpi.linuxgccrelease" (in my Open MPI compilation :scons bin mode=release cxx=gcc cxx_ver=4.6" ALL executables are both ".mpi." and non-mpi, which is strange as not all are parallelized) according to the command line:

Hi,

I have a question about output file test_loop_output.fasc in
an example of Cyclic Coordinate Descent loop closure - loop_modeling.py.
Here we have rmsd and Lrmsd, what is the difference?
In manual you can find that Lrmsd is the rmsd of all loops in the reference
frame of the fixed protein structure.
What does it means? What is rmsd?
How to find rmsd for all loop backbone atoms?

Thank you,

Victor

Hi,

Just curious if there is or there will be a flag to use Roland's 2010 Rotamer library within Rosetta. We have been replacing the 2008 binaries with data using the 2010 library and then using the 2008 flag, which works well enough. I'm still learning C++, or I would try and implement it myself.

Also, if it does already work within Rosetta, where would I find it within the code, and which level of smoothing was used? (optim, 5%, 20%)? We have been using optim (with the neighbor-dependent ramachandran flag) across most of Rosetta's apps and it seems to work well.